Eight months after Rosen went public with news of Alphas, the government has hushed him up, locked him in a sanitarium, and turned the existence of Alphas into an urban legend. His team of Alphas have gone their separate ways, but when a prison riot of violent Alphas occurs, the government needs Rosen and Rosen needs his teammates.

The team search for an Alpha who kills and has superspeed abilities, but he soon comes looking for them when he believes that Rosen may be able to cure his accelerated aging.

When tracking down an Alpha who kills other Alphas, Bill goes undercover at a fight club for Alphas. A young girl, Kat, takes an interest in him and offers to show him how to control his abilities. Meanwhile, Rosen continues his investigation of Stanton Parish, the team gets a new tac officer, and Gary moves away from home.

The team discovers that Nina is out of control and using her powers to control anyone and everyone that she needs to so that she can get what she wants.

Rosen checks on a former Alpha patient at a hospital and the team discovers bizarre phenomenon leading to Rachel's abduction. Meanwhile, Gary receives an unexpected victim and Kit starts to remember her past.

Rosen traces Skylar to an isolated Alpha colony to get her help examining Stanton's photic stimulator. However, Stanton sends a team to recover the machine and the colonists are caught in the middle.

Jason Miller, an Alpha with the ability to control humans through infrasound, comes into his own when he takes over his high school. To stop him, Rosen must ally with Stanton Parish to save Jason's victims before it's too late.

The team learns of a street drug that gives normal humans Alpha-level invulnerability... and can prove lethal. Meanwhile, Rosen tracks down the mole and faces a difficult decision, and Cameron tries to cope with his son.

Hicks turns defector to be with the woman he loves and begins working for Stanton. Meanwhile, Rosen and the others discover that Stanton plans to use experimental grenades to generate an electrical storm and wipe out millions in Manhattan.

While the team tries to cope with Danielle's death, a mysterious woman drops a baby off at the office and Gary is strangely drawn to protecting it.

While Cameron and Kat track down an Alpha who may hold the key to Stanton's plans, Senator Burton discovers that Nina and Rosen pushed her and threatens retaliation. Meanwhile, Gary goes to the hospital when his mother is involved in a car accident.

While most of the team goes underground to interrogate one of Stanton's people, Bill, Gary, and Kat track down Skylar, who has inadvertently manufacturing a device that will let Stanton initiate his master plan.

While the team tries to stop Stanton Parish's master plan to wipe out the population of nineteen major American cities, Rosen goes on a personal quest to get revenge on the man who killed his daughter.